JAL-4061 tests, bugfixes and TODOs for matching feature(s) and descriptions incrementally

[jalview.git] / test / jalview / analysis / FinderTest.java

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 42225e8..62e219d 100644 (file)
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -40,7 +40,9 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
@@ -81,6 +83,12 @@ public class FinderTest
             DataSourceType.PASTE);
     av = af.getViewport();
     al = av.getAlignment();
+    al.getSequenceAt(0).addSequenceFeature(
+            new SequenceFeature("BBBB", "FeatureB", 9, 11, ""));
+    al.getSequenceAt(3).addSequenceFeature(
+            new SequenceFeature("BBAB", "FeatureA", 1, 3, ""));
+    al.getSequenceAt(3).addSequenceFeature(
+            new SequenceFeature("AAAA", "FeatureA", 9, 11, ""));
   }
 
   @AfterMethod(alwaysRun = true)
@@ -925,4 +933,36 @@ public class FinderTest
     assertEquals(match.getStart(), 7); // H (there is no G)
     assertEquals(match.getEnd(), 7);
   }
+
+  @Test(groups = "Functional")
+  public void testFind_featuresOnly()
+  {
+    Finder f = new Finder(av);
+    // no match when not searching feature descriptions
+    f.findAll("Feature", false, false, false, true);
+    assertEquals(f.getSearchResults().getCount(), 0);
+
+    // no match when case sensitive on feature descriptions
+    f.findAll("feature", true, false, true, true);
+    assertEquals(f.getSearchResults().getCount(), 0);
+
+    // search feature descriptions - all match
+    f.findAll("Feature", false, false, true, true);
+    assertEquals(f.getSearchResults().getCount(), 3);
+
+    List<SequenceI> seqs = f.getSearchResults().getMatchingSubSequences();
+    // assume order is preserved in results
+    assertEquals(al.getSequenceAt(0).getDatasetSequence(),
+            seqs.get(0).getDatasetSequence());
+    assertEquals(seqs.get(0).getStart(), 9);
+    assertEquals(seqs.get(0).getEnd(), 11);
+    assertEquals(al.getSequenceAt(3).getDatasetSequence(),
+            seqs.get(1).getDatasetSequence());
+    assertEquals(seqs.get(1).getStart(), 9);
+    assertEquals(seqs.get(1).getEnd(), 11);
+    assertEquals(al.getSequenceAt(3).getDatasetSequence(),
+            seqs.get(2).getDatasetSequence());
+    assertEquals(seqs.get(2).getStart(), 1);
+    assertEquals(seqs.get(2).getEnd(), 3);
+  }
 }